Package ffx.potential.parameters
@ParametersAreNonnullByDefault
package ffx.potential.parameters
The Parameters package stores force field atom types, bond types, etc, and keywords that define
the potential.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
-
ClassDescriptionThe AngleTorsionType class defines one angle-torsion energy type.The AngleType class defines one harmonic angle bend energy term.Angle function types include harmonic or sextic.Angle modes include Normal or In-PlaneThe AtomType class represents one molecular mechanics atom type.All force field types should extend the BaseType class.The BioType class maps PDB identifiers to atom types.The BondType class defines one harmonic bond stretch energy term.Describes the function used by the bond.The ChargeType class defines a partial atomic charge type.The ForceField class organizes parameters for a molecular mechanics force field.Available force fields.The ImproperTorsionType class defines an improper torsion.The MultipoleType class defines a multipole in its local frame.The local multipole frame is defined by the Z-then-X or Bisector convention.The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.The PolarizeType class defines an isotropic atomic polarizability.A BaseType for relative solvation energies (intended for nonstandard amino acids).The SoluteType class defines one implicit solvent radius.The StretchBendType class defines one out-of-plane angle bending energy type.The StretchTorsionType class defines one stretch-torsion energy type.Utilities for interpolating between Amino Acid protonation and tautomer states.Constant
CysteineAtomsConstantHistidineAtomsConstantlysineAtomsAmino acid protonation reactions.The TorsionTorsionType class defines a Torsion-Torsion spline.The TorsionType class defines a torsional angle.Torsion modes include Normal or In-PlaneThe UreyBradleyType class defines one harmonic UreyBradley cross term.The VDWPairType class defines a van der Waals Pair type.The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.Epsilon combining rule.Radius combining rule.Radius size in the parameter file (radius or diameter).Radius type in the parameter file (R-Min or Sigma).VDW Type.Torsion modes include Normal or In-Plane